It's actually quite easy.  Most of the videos you've probably seen are very close up - which is great after you gave your ships their attack orders, but usually you will be zoomed out a bit more and you can just bandbox your ships, or even easier, use the empire tree on the left side of the screen. 

The empire tree (which is often turned off in the videos) allows you to quickly see every ship in a battle in icon form - and you can do almost everything with the icon that you can do with the actual ship.

Also, the unit AI is quite good. Tell your ships where you want them to go, then turn on 'auto-attack' or any 'auto-ability' and they will go about their business - giving you time to focus on your elite group, your capital ships, building your trade empire, diplomatic relations, or whatever.